Alternative Splicing Novel lncRNAs and Their Target Genes in Ovine Skeletal Muscles

Document Type : Research Articles

Authors

• Saad Badday Betti ^{1, 2}
• Mojtaba Tahmoorespur ¹
• Ali Javadmanesh ^{1, 3}

¹ Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Iran

² Chief of Agricultural Engineers, Ministry of Agriculture, Baghdad, Iraq

³ Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran

https://doi.org/10.22067/jcmr.2022.74635.1027

Abstract

Long non-coding RNAs (lncRNAs) compose a plentiful category of transcripts that have gained increasing importance because of their roles in different biological processes. Although the function of most lncRNAs remains unclear. They are implicated in epigenetic regulation of gene expression, including muscle development and differentiation. We aimed to identify the effect of novel lncRNAs (Alternatively spliced) and their target genes on two stages of sheep skeletal muscle growth and development. FastQC files have been used to examine the quality control and the Trimmomatic program for trimming low-quality reads from twelve longissimus dorsal muscle tissue samples (including six young and six old from Texel sheep). Hisat2, Cufflink, Cuffmerge, and Cuffdiff investigated the expression levels. Novel lncRNAs (Alternative spliced) were distinguished using NONCODE databases and Cuffcompare software. In addition, the lncRNA–mRNA interactions and regulatory network visualization were identified via RIsearch and Cytoscape software, respectively. Those 139 novel lncRNA (Alternative spliced) transcripts had been recognized, probably 65 lncRNAs interacted with their target genes and regulated sheep skeletal muscle growth and development. Three novel lncRNA transcripts (TCONS_00041386, TCONS_00050059, and TCONS_00056428) showed a strong association and five transcripts (TCONS_00055761, TCONS_00055762, TCONS_00055763, TCONS_00055764, and TCONS_00055770) had made complex network correlations with mRNAs. Our research provided more knowledge of the associated mechanisms with novel lncRNAs, which could play a role in regulating sheep skeletal muscle tissue development and growth.

Keywords

• Regulatory Network
• Novel lncRNAs
• Skeletal Muscle
• Alternative Splicing
• Gene Expression

20.1001.1.20089147.2022.13.2.5.4

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